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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttattcttatatttcgatgtgtcattttccttaccattcctagataaatcatgttaacatgtgttttgtacttttgtgatgcagGCTACAAGGACCCAGAGCCTTCAAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGAT

Basic information

species Oryza sativa
transcript LOC_Os01g44040.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
----------gttggttattcttatatttcgatgtgtcattttcct-taccattcctagataaatcatgttaacatgtgttttgtacttttgtgatgcagGCTACAAGGACCCAGAGCCTTCAAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGAT------
          || |  | ||   |  |||| |  ||   |  |  | ||   || |  | |   |  ||  ||    |  ||   | |||| ||  ||||| || |      | || ||| ||||  |  |  | || |   ||||||||||||||||| ||||||| |||||||| || || ||||| |||||||||||      
gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATA------CTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC

upper sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
---gttggttattcttatatttcgatgtgtcattttccttaccattcctagataa-atcatgttaacatgtgttttgtacttttgtgatgcagGCTACAAGG-ACCCAGAGCCTTCAAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGAT------
    |||  | || |    || | || |   | ||   || | | |   || | | ||  |||| ||      |   || || |    |  | |   || |  |  | || ||| ||||  |  |  | || |   ||||||||||||||||| ||||||| |||||||| || || ||||| |||||||||||      
gcttttgtatgttgtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttactgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88721652|gb|CI744951.1|CI744951
EST:     AATTCCTGGTGTATTTGAACTGCTGTGGAGTCCATTTACATTTCTGCTAG                         GCTACAAGGACCCAGAGCCTTCAAAAGCAAACTTACCACTGTTGCATGAGT
genomic: AATTCCTGGTGTATTTGAACTGCTGTGGAGTCCATTTACATTTCTGCTAGgttggttatt ... tgtgatgcagGCTACAAGGACCCAGAGCCTTCAAAAGCAAACTTACCACTGTTGCATGAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaccattcctagataaatcatgttaacatgtgttttgtacttttgtgatgcagGCTACAAGGACCCAGAGCCTTCAAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGAT
                      tgttaac  putative branch site (score: 2)
                                       tactttt  putative PPT
              ataaatcatgttaa  TA-rich tract